Recommended Readings: Coleen Murphy, Ph.D. Friday April 26, 2019

                                               Friday Lectures

Friday, April 26, 2019  3:45 p.m

Caspary Auditorium

Coleen Murphy Ph.D.

Professor and Director

Glenn Center for Quantitative Aging Research

Princeton University

Transgenerational Inheritance of Pathogen Avoidance (or, How Getting Food Sickness Might Save Your Species)


Recommended Readings:

Science News

In a tiny worm, a close-up view of where genes are working. September 18, 2018. Science Daily

Empirical Articles

Moore RS, Kaletsky R, Murphy Coleen Tara. (2018). C. elegans pathogenic learning confers multigenerational pathogen avoidance. BioRxiv

Tabuchi, Tomoko M.; Rechtsteiner, Andreas; Jeffers, Tess E.; et al. (2018). Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis. NATURE COMMUNICATIONS. 9

Kaletsky, Rachel; Yao, Victoria; Williams, April; et al. (2018). Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLOS GENETICS. 14 (8)

Review Paper

Templeman, Nicole M.; Murphy, Coleen T. (2018). Regulation of reproduction and longevity by nutrient-sensing pathways. JOURNAL OF CELL BIOLOGY. 217 (1): 93-106

Book Chapter

Shi, Cheng; Murphy, Coleen T. (2017). Reproductive Ageing. AGEING: LESSONS FROM C. ELEGANS. 5: 137-162

Recommended Readings: Shai Shaham, Ph.D., Monday April 16, 2018

Monday Lectures

Monday, April 16, 2018  4:00 p.m.

Carson Family Auditorium

Shai Shaham, Ph.D.

Richard E. Salomon Family Professor and Head

Laboratory of Developmental Genetics

The Rockefeller University

Uncovering Cell Death Treasure Hiding in Plain Sight

Recommended Readings:

Science News

Brandon Specktor. See How a Single Cell Dies in Gory, Intricate Detail. (March 28, 2018). Live Science

Empirical Articles

Ghose P, Rashid A, Insley P, Trivedi M, Shah P, Singhal A, Lu Y, Bao Z, Shaham S. (2018). EFF-1 fusogen promotes phagosome sealing during cell process clearance in Caenorhabditis elegans. NATURE CELL BIOLOGY. 20 (4):393-399

Malin, Jennifer A.; Kinet, Maxime J.; Abraham, Mary C.; et al. (2016). Transcriptional control of non-apoptotic developmental cell death in C-elegans. CELL DEATH AND DIFFERENTIATION. 23 (12): 1985-1994

Schwendeman, Andrew R.; Shaham, Shai. (2016). A High-Throughput Small Molecule Screen for C-elegans Linker Cell Death Inhibitors. PLOS ONE. 11 (10) 

Kinet, Maxime J.; Malin, Jennifer A.; Abraham, Mary C.; et al. (2016). HSF-1 activates the ubiquitin proteasome system to promote non-apoptotic developmental cell death in C. elegans. ELIFE. 5

Blum, Elyse S.; Abraham, Mary C.; Yoshimura, Satoshi; et al. (2012). Control of Nonapoptotic Developmental Cell Death in Caenorhabditis elegans by a Polyglutamine-Repeat Protein. SCIENCE. 335 (6071): 970-973

Review Papers

Kutscher, Lena M.; Shaham, Shai (2017). Non-apoptotic cell death in animal development. CELL DEATH AND DIFFERENTIATION. 24 (8): 1326-1336

Blum, Elyse S.; Schwendeman, Andrew R.; Shaham, Shai. (2013). PolyQ disease: misfiring of a developmental cell death program? TRENDS IN CELL BIOLOGY. 23 (4): 168-174  

Book Chapters

Malin, Jennifer Zuckerman; Shaham, Shai. (2015). Cell Death in C. elegans Development. CURRENT TOPICS IN DEVELOPMENTAL BIOLOGY. 114: 1-42

Kinet, Maxime J.; Shaham, Shai. (2014). Noncanonical Cell Death in the Nematode Caenorhabditis elegans. METHODS IN ENZYMOLOGY. 545: 157-180


Recommended Readings: Cori Bargmann, Ph.D., April 4

Monday Lecture Series
Monday, April 4
4:00 p.m., Carson Family Auditorium (CRC)

Cori Bargmann, Ph.D.
Torsten N. Wiesel Professor and Head,
Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Themes and variations in circuits and behavior

Recommended Readings

Empirical Papers

Flavell, S. W., Pokala, N., Macosko, E. Z., Albrecht, D. R., Larsch, J., & Bargmann, C. I. (2013). Serotonin and the neuropeptide PDF initiate and extend opposing behavioral states in C. elegans. Cell, 154(5), 1023-1035. doi: 10.1016/j.cell.2013.08.001.

Gordus, A., Pokala, N., Levy, S., Flavell, S. W., & Bargmann, C. I. (2015). Feedback from network states generates variability in a probabilistic olfactory circuit. Cell, 161(2), 215-227. doi: 10.1016/j.cell.2015.02.018.

Jin, X., Pokala, N., & Bargmann, C. I. (2016). Distinct circuits for the formation and retrieval of an imprinted olfactory memory. Cell, 164(4), 632-643. doi: 10.1016/j.cell.2016.01.007.

Review Papers

Bargmann, C. I. (2006). Chemosensation in C. elegans. WormBook. doi/10.1895/wormbook.1.123.1

Bargmann, C. I., & Marder, E. (2013). From the connectome to brain function. Nature Methods, 10(6), 483-490. doi: 10.1038/nmeth.2451

Recommended Readings: Gary Ruvkun, Ph.D. October 24

Friday Lecture Series
Friday, October 24, 2014
3:45 p.m., Caspary Auditorium

Gary Ruvkun, Ph.D.
Hans-Hermann Schoene Distinguished Investigator and Professor,
Department of Genetics,
Harvard Medical School

C. elegans Surveillance of Conserved Cellular Components to Detect and Defend Pathogen Attacks, Real or Imagined

Recommended Readings

Empirical Articles

Liu, Y., Samuel, B. S., Breen, P. C., & Ruvkun, G. (2014). Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature, 508(7496), 406–410. doi:10.1038/nature13204

Melo, J. A, & Ruvkun, G. (2012). Inactivation of conserved C. elegans genes engages pathogen- and xenobiotic-associated defenses. Cell, 149(2), 452–466. doi:10.1016/j.cell.2012.02.050

Shore, D. E., Carr, C. E., & Ruvkun, G. (2012). Induction of cytoprotective pathways is central to the extension of lifespan conferred by multiple longevity pathways. PLoS Genetics, 8(7), e1002792. doi:10.1371/journal.pgen.1002792

Review Papers

Shore, D. E., & Ruvkun, G. (2013). A cytoprotective perspective on longevity regulation. Trends in Cell Biology, 23(9), 409–420. doi:10.1016/j.tcb.2013.04.007

Recommended Readings: Diana Libuda, Ph.D. Wednesday, January 22

Wednesday, January 22, 2014
4:00 p.m., Carson Family Auditorium

Diana Libuda, Ph.D.
Postdoctoral Fellow
Department of Developmental Biology
Stanford University School of Medicine

Making the right decision: repairing DNA breaks during meiosis

Recommended Readings:

Empirical Articles

Libuda, D. E., Uzawa, S., Meyer, B. J., & Villeneuve, A. M. (2013). Meiotic chromosome structures constrain and respond to designation of crossover sites. Nature, 502(7473), 703–706. doi:10.1038/nature12577

Martinez-Perez, E., & Villeneuve, A. M. (2005). HTP-1-dependent constraints coordinate homolog pairing and synapsis and promote chiasma formation during C . elegans meiosisGenes & Development, 19(22), 2727–2743. doi:10.1101/gad.1338505.recombination

Rosu, S., Libuda, D. E., & Villeneuve, A. M. (2011). Robust crossover assurance and regulated interhomolog access maintain meiotic crossover number. Science, 334(6060), 1286–1289. doi:10.1126/science.1212424

Yokoo, R., Zawadzki, K. A., Nabeshima, K., Drake, M., Arur, S., & Villeneuve, A. M. (2012). COSA-1 reveals robust homeostasis and separable licensing and reinforcement steps governing meiotic crossovers. Cell, 149(1), 75–87. doi:10.1016/j.cell.2012.01.052

Review Papers

Martinez-Perez, E., & Colaiácovo, M. P. (2009). Distribution of meiotic recombination events: talking to your neighbors. Current Opinion in Genetics & Development, 19(2), 105–112. doi:10.1016/j.gde.2009.02.005

Page, S. L., & Hawley, R. S. (2003). Chromosome choreography: the meiotic ballet. Science, 301(5634), 785–789. doi:10.1126/science.1086605

Recommended Readings: Kang Shen, Ph.D.

Friday Lecture Series

Extracellular and Intracellular Mechanisms of Synapse Patterning in C. elegans

Kang Shen, Ph.D., M.P.H., associate professor,

department of biological sciences, Stanford University

 February 22, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Allen, P. B., Sgro, A. E., Chao, D. L., Doepker, B. E., Edgar, J. S., Shen, K., & Chiu, D. T. (2008). Single-synapse ablation and long-term imaging in live C. elegans. Journal of Neuroscience Methods, 173(1), 20-26

Crane, M. M., Stirman, J. N., Ou, C. -., Kurshan, P. T., Rehg, J. M., Shen, K., & Lu, H. (2012). Autonomous screening of C. elegans identifies genes implicated in synaptogenesis. Nature Methods, 9(10), 977-980

Klassen, M. P., Wu, Y. E., Maeder, C. I., Nakae, I., Cueva, J. G., Lehrman, E. K., . . . Shen, K. (2010). An arf-like small G protein, ARL-8, promotes the axonal transport of presynaptic cargoes by suppressing vesicle aggregation. Neuron, 66(5), 710-723

Maeder, C. I., & Shen, K. (2011). Genetic dissection of synaptic specificity. Current Opinion in Neurobiology, 21(1), 93-99

Margeta, M. A., Wang, G. J., & Shen, K. (2009). Clathrin adaptor AP-1 complex excludes multiple postsynaptic receptors from axons in C. elegans. Proceedings of the National Academy of Sciences of the United States of America, 106(5), 1632-1637


Recommended Readings: Shai Shaham PH.D. Monday, March 26, 2012

A New C. elegans Cell Death Program: Implications for

Neurodegeneration and Cancer

Shai Shaham, Ph.D.

Laboratory of Developmental Genetics

The Rockefeller University

4:00 p.m. Monday, March 26, 2012    Refreshments  3:45  Abby Lounge

Caspary Auditorium

Recommended readings:

Blum, E.S., Abraham, M.C., Yoshimura, S., Lu, Y., and S. Shaham.  2012.  Control of nonapoptotic developmental cell death in Caeanorhabditis elegans by a polyglutamic-repeat proteinScience.  335(6071):970-973.  DOI: 10.1126/science.1215156

 McCall, K.  2010.  Generic control of necrosis – another type of programmed cell death Current Opinion in Cell Biology.  22(6):882-888.  DOI: 10.1016/

 Yuan, J. and G. Kroemer.  2010.  Alternative cell death mechanisms in development and beyond.  Genes & Development.  24(23):2592-2602.  DOI: 10.1101/gad.1984410

 Vlachos, M. and  N. Tavernarakis.  2010.  Non-apoptotic cell death in Caenorhabditis elegans.  Developmental Dynamics.  239(5, S1):1337-1351.   DOI: 10.1002/dvdy.22230

 Miguel-Aliaga, I. and T. Stefan.  2009.  Programmed cell death in the nervous system – a programmed cell fate?  Current Opinion in Neurobiology.  19(2):127-133   DOI: 10.1016/j.conb.2009.04.002

Blum, E.S., M. Driscoll, and S. Shaham.  2008.  Noncanonical cell death programs in the nematode Caenorhabditis elegans.  Cell Death and Differeentiation.  15(7):1124-1131.  DOI: 10.1038/cdd.2008.56

 Abraham, M. C., L. Yun, and S. Shaham.  2007.  A morphologically conserved nonapoptotic program promotes linker cell death in Caenorhabiditis elegans.   Development Cell.  12(1):73-86.  DOI:  10.1016/j.devcel.2006.11.012


A 3D Atlas of C. elegans

Nature Methods
Published online: 16 August 2009 | doi:10.1038/nmeth.1366

 A 3D digital atlas of C. elegans and its application to single-cell analyses

Fuhui Long1,3, Hanchuan Peng1,3, Xiao Liu2, Stuart K Kim2 & Eugene Myers1


We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.

 1. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

 2. Department of Developmental Biology, Stanford University Medical Center, Stanford, California, USA.

3.  These authors contributed equally to this work.

Correspondence to: Eugene Myers1 e-mail:

Recommended Readings: Alexander Soukas, M.D., Ph.D.; July 20, 2009

Monday Lecture Series

Genetics of lipid storage: lessons learned from C. elegans

Alexander Soukas, M.D., Ph.D.

Instructor, Dept. of Medicine, Massachusetts General Hospital, Harvard Medical School

Monday, July 20, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Soukas, A. A., E. A. Kane, C. E. Carr, J. A. Melo, and G. Ruvkun. 2009. Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegans. Genes and Development. 23(4):496-511.


Greer, E. R., C. L. Pérez, M. R. Van Gilst, B. H. Lee, and K. Ashrafi. 2008. Neural and molecular dissection of a C. elegans sensory circuit that regulates fat and feeding. Cell Metabolism. 8(2):118-131.


Srinivasan, S., L. Sadegh, I. C. Elle, A. G. L. Christensen, N. J. Faergeman, and K. Ashrafi. 2008. Serotonin regulates C. elegans fat and feeding through independent molecular mechanisms. Cell Metabolism. 7(6): 533-544.


Wang, M. C., E. J. O’Rourke, and G. Ruvkun. 2008. Fat metabolism links germline stem cells and longevity in C. elegans. Science. 322(5903):957-960.


Xie, T. 2008. Physiology: Burn fat, live longer. Science. 322(5903):865-866.


Zhang, J., C. Yang, C. Brey, M. Rodriguez, Y. Oksov, R. Gaugler, E. Dickstein, C. -H Huang, and S. Hashmi. 2009. Mutation in Caenorhabditis elegans krüppel-like factor, KLF-3 results in fat accumulation and alters fatty acid composition. Experimental Cell Research (article in Press).






Related Readings: Leonid Kruglyak PhD

Special Seminar Series:  Systems Biology

Learning C. elegans Biology from Natural Genetic Variation

Leonid Kruglyak, Ph.D.

Professor of Ecology and Evolutionary Biology

Lewis-Sigler Institute for Integrative Genomics

Princeton University

Welch Hall, Level 2  4:00 p.m   Refreshments: 3:45 

Recommended Articles:

Zhu, Jun; Zhang, Bin; Smith, Erin N.; Drees, Becky; brem, Rachel B.; Krulyak, Leonid; Bumgarner, Roger E.; Schadt, Eric E.  2008.  Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.  Nature Genetics.   40(7): 854-861.


Smith, Erin N.; Kruglyak, Leonid.  2008.  Gene-environment interaction in yeast gene expression. PLoS Biology.  6(4):e83


Seidel, Hannah S.; Rockman, Matthew V.; Kruglyak, Leonid.  2008.  Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science   319 (5863): 589-594


Rockman, Matthew V.; Kruglyak, Leonid.  2006. Genetics of global gene expression.  Nature Reviews Genetics.  7(11):862-872.


Kroymann, Juergen; Mitchell-Olds, Thomas.  2005.  Epistasis and balanced polymorphism influencing complex trait variation.  Nature  435(7038): 95-98.


Wright, Stephen I.; Gaut, Brandon S.  2005.  Molecular population genetics and the search for adaptive evolution in plants.  Molecular Biology and Evolution.  22(3):505-519